His confirmation Monday drew scrutiny and nine dissenters. Now Veterans Affairs Secretary Robert Wilkie must face the real challenge: repairing the sprawling agency that serves the nation’s veterans, including 9 million who receive health care benefits through the department.

The second-largest federal agency is embarking on two major initiatives — a reorganization of its private medical care options and a $15.8 billion electronic health records project — at the same time that it seeks to fill key positions overseeing them.

The Senate may have confirmed Wilkie, 86-9, but the $187 billion agency still lacks permanent officials in three other leading roles — deputy secretary, undersecretary for health and chief information officer. Many believe the vacancies could hinder the department’s efforts to right itself as it works to improve lengthy wait times and address concerns about its quality of care.

The VA has been a revolving door for senior officials for years as it struggles to solve systemic problems plaguing its more than 1,200 medical care facilities.

Watch: Who Is Robert Wilkie?

“I just think that no one can do it alone, and Robert Wilkie is going to have to make sure he has a strong staff to help support him,” said Lou Celli, executive director of government and veterans affairs for the American Legion.

The workload would be a heavy lift for any department, but the VA’s history of problems and the sensitive nature of veteran care has lawmakers on edge. Montana Democratic Sen. Jon Tester told Wilkie at his June 27 Senate confirmation hearing that he would be taking the helm during “unprecedented times” at the VA.

But department officials have defended the VA’s ability to meet expectations, saying that lower-level employees carrying out the agency’s mission remain dedicated and on track to meet quickly approaching deadlines.

This spring, the VA launched the two massive projects in a bid to remake its core operations controlling veteran health care. One is a $21.4 billion reorganization combining the department’s seven disparate community care programs that allow veterans to see private providers outside of VA facilities.

The overhaul was the central focus of the so-called VA Mission Act, which President Donald Trump signed in June. One of the most important tasks facing the department is mapping out eligibility standards for veterans who previously received care across the different programs, Celli said.

Budgeting will also be key, he said, since shortfalls helped lead to a 2014 scandal at the Phoenix VA hospital, where a number of veterans died while waiting for appointments on the facility’s secret wait list. That scandal led Congress to expand private medical care several times, culminating with the overhaul that Trump just signed.

Celli says he hopes the agency does not have to prioritize based on budget versus need.

The new law also includes a $6.7 billion expansion of a program aiding family caregivers, as well as a wholesale review of all of the department’s facilities that could further remake the VA in future years. The assessment will be conducted by the VA and a new commission to recommend whether hospitals or other facilities should be closed, expanded or altered.

The second major project is the $15.8 billion, 10-year endeavor to replace the VA’s electronic health record system with one that is interoperable with that of the Department of Defense as well as private doctors and hospitals across the country. Wilkie, who was acting VA secretary at the time, inked the deal with health IT company Cerner in May.

Additionally, the VA is dealing with myriad other controversies. The department suffers from a shortage of frontline medical personnel, a problem that the private sector also faces but one that complicates efforts to improve outcomes at VA’s heavily scrutinized facilities. Nursing home ratings released in June showed that nearly half earned the lowest possible quality score, although nearly all received the highest score on staffing levels.

Expansion of the private care program has reinvigorated fears that more funds will be shifted away from VA facilities.

“It’s extremely important that we sustain a strong and healthy infrastructure at the Department of Veterans Affairs,” Celli said.

Challenges at the top

Wilkie’s work on the electronic health records project will be closely evaluated.

The department is set to adopt the Defense Department’s platform, MHS Genesis, with significant modifications in order to interact with private providers, but the DOD’s rollout has been rocky. The project director halted the platform’s testing at a fourth site in April, citing “significant problems” at the first three pilot sites. The VA is set to debut its version of the software at initial testing sites by March 2020.

“Leadership will make or break this project,” House Veterans’ Affairs ranking Democrat Tim Walz of Minnesota said last month at the committee’s first oversight hearing on the project.

The onus will fall to Wilkie, but he has some controversies of his own.

A recent profile in The Washington Post detailed Wilkie’s defense of the Confederate flag, and his history of serving on the staff of divisive politicians like former North Carolina GOP Sen. Jesse Helms. A former member of the Sons of Confederate Veterans, Wilkie said he stopped participating in Confederate events once it became politically divisive.

The allegations weren’t serious enough to derail him during his Senate Veterans’ Affairs nomination hearing in June nor bar him from earning the committee’s approval in July.

A lawyer and an intelligence officer in the Air Force Reserve, Wilkie grew up on Fort Bragg as the son of a Vietnam veteran who was seriously wounded in combat. He also previously served in the Navy Reserves.

In the George W. Bush administration, Wilkie worked on the National Security Council under Condoleezza Rice, as well as for former Defense secretaries Donald Rumsfeld and Robert Gates.

This marked Wilkie’s third tour of the Senate confirmation process. At his hearing, Wilkie specifically cited his Defense Department work to reduce wait times within its Defense Health Agency, assuring South Dakota Republican Mike Rounds, a vocal skeptic of the recently enacted VA private care overhaul, that he was capable of reducing wait times for veterans.

Wilkie also pledged to “walk the post” as secretary by visiting different branches of the department in person. During the two months he spent as acting secretary, Wilkie visited five separate facilities.

“I mentioned in the first statement that I gave at VA that it has to be a bottom-up organization — that anyone who sits in the secretary’s chair and claims he has the answers should not be there,” Wilkie said.

Months of turmoil

Some of the vacancies themselves are embroiled in controversy.

The VA had lacked a confirmed leader since March, when Trump ousted Obama-era holdover David Shulkin from the role amid questions about taxpayer-funded travel with his wife and revelations that he improperly accepted Wimbledon tickets. (Shulkin repaid the agency for his wife’s travel and pledged to pay for the tickets.)

Shulkin also accused Trump political appointees of organizing a revolt against him, alleging he was fired and contradicting the White House’s claim that he had resigned. In response to a Freedom of Information Act request, the VA said it had no resignation letter. If Shulkin was fired, it raises questions about whether Trump was legally allowed to bypass Shulkin’s deputy in favor of Wilkie as acting secretary. That consequently casts doubt on the legality of the Cerner contract that Wilkie signed.

Shulkin’s abrupt departure triggered a turnover in senior officials who otherwise would have left at the beginning of the Trump administration, say advocacy groups. The result is a lack of permanent leadership, including the chief information officer who would oversee the electronic health records implementation.

The acting CIO, Camilo Sandoval, stands accused by a former female colleague, Jessica Denson, of harassment and discrimination during their time on the Trump campaign. The House Veterans’ Affairs Committee declined to invite Sandoval to testify at the first hearing on the records project on June 26.

Acting Secretary Peter O’Rourke assured the committee that he remains confident in Sandoval’s ability to perform his duties, and VA spokesman Curt Cashour said a permanent CIO candidate is being vetted by the White House.

Also missing is an undersecretary for health, a post temporarily filled by former Agency for Healthcare Research and Quality Director Carolyn Clancy, who previously served in the position. O’Rourke replaced Clancy with Richard Stone, who is also serving in an acting capacity.

Questions remain over who will fill the positions and when they will assume the roles. The department will be making announcements on several senior positions in the coming weeks, a senior VA official said.

O’Rourke indicated to the House committee that he was unaware of the status of the positions, saying that the department has sent multiple candidates to the White House for approval.

Dan Caldwell, executive director for the Koch network-backed group Concerned Veterans for America, said the White House has made multiple job offers, but they have fallen through.

Wilkie, for his part, told the Senate VA Committee that he did not have a list of people in mind for the empty positions.

Mixed reviews

Watchdogs have consistently cited lack of leadership as the VA’s main problem, and it’s hard to see how extended vacancies won’t exacerbate the department’s entrenched issues.

But initial reports from department officials indicate the agency is so far on track for at least the health-records overhaul.

Officials outlined details of governance structure and planning to the House VA Committee in the June hearing, and said interagency meetings were happening regularly. Cashour said the VA was “absolutely” capable of handling the project.

“VA’s electronic health record modernization efforts are being led by virtually the same team that successfully finalized the contract with Cerner — an unprecedented achievement in VA history,” he said.

Cashour similarly disputed the notion that the VA is ill-equipped to handle obligations under the recent private care law. Lawmakers — particularly Democrats — have questioned whether the VA has the resources to handle the overhaul of the community care programs, in addition to an influx of veterans under the caregiver expansion.

“The concerns about the Mission Act are unfounded, as the regulations governing the implementation of the Mission Act won’t be completed until long after a permanent secretary is in place,” Cashour said, adding that the Trump administration has been quicker to fill positions than the Obama administration.

Veterans’ groups believe Wilkie has the credentials necessary to lead the agency.

His background is far more reassuring to lawmakers and advocacy groups than Jackson’s, who had never managed anything on par with the VA. His brief stint as acting secretary also allowed him to lay some groundwork for the two projects.

“I don’t think he would go into this job with a very steep learning curve as a result,” Caldwell said.

Wilkie has also made himself available to veterans groups, promising to tackle administrative problems that led to vacancies in the department’s lower ranks as well.

As the VA opens the door further on private care, ensuring the continued success of the department’s internal operations will become more important to advocacy groups.

But the concerns extend beyond where a veteran receives care. Paul Rieckhoff, executive director of the Iraq and Afghanistan Veterans of America, said traditional veterans service organizations under Trump are increasingly sidelined in favor of more political groups seeking to increase privatization.

“Our biggest concern is that the very soul of the VA is being attacked,” he said. “The very essence of what VA does and its very mission is being eroded.”

The shortfalls within the VA have been well documented. Now it’s up to the department, and likely Wilkie, to act on them.

“Mr. Wilkie, there are no excuses anymore,” Senate Veterans’ Affairs Chairman Johnny Isakson, a Georgia Republican, said at his confirmation hearing. “Failure is not an option.”